Acutally, the autorecon flags require that the subcortical segmentation be done (ie, you can't use -nosubcortseg with -autorecon)

Nick Schmansky wrote:

Margo,

In looking at the directory:

/autofs/space/lucy_002/users/margo/subjects/avm004/mri/

it appears the file norm.mgz does not exist, which accounts for the error running autorecon2.

Normally, the file norm.mgz is created in the autorecon1 stage, so I'm not sure why it wasn't created, but you can create norm.mgz by running the following two commands in your .../avm004/mri/ directory:

mri_em_register -mask brain.mgz -p .5 nu.mgz \ $FREESURFER_HOME/average/RB40_talairach_2005-07-20.gca \ transforms/talairach.lta

mri_ca_normalize -mask brain.mgz nu.mgz \ $FREESURFER_HOME/average/RB40_talairach_2005-07-20.gca \ transforms/talairach.lta norm.mgz

Nick

On Tue, 2006-01-03 at 10:27 -0500, Margo McKenna Benoit wrote:

...

Hi, I'm following up on an earlier email about the mri_ca_normalize step of autorecon2. I am getting an error while running autorecon2 in the developmental freesurfer version on tkmeg at the nmr center. The command I ran was: <recon-all-nmr -subjid avm004 -autorecon2 -nosubcortseg -hemi lh -mail margo> and the output error is below. My directory is /space/lucy/2/users/margo/subjects/ Any advice would be greatly appreciated. Thanks, Margo

INFO: SUBJECTS_DIR is /autofs/space/lucy_002/users/margo/subjects Actual FREESURFER_HOME /autofs/space/freesurfer/centos4.0/dev2-0-0 -rw-rw-r-- 1 margo smsgp 203951 Dec 22 11:03 /autofs/space/lucy_002/users/margo/subjects/avm004/scripts/recon-all.log Linux tkmeg 2.6.9-22.0.1.ELsmp #1 SMP Thu Oct 27 13:14:25 CDT 2005 i686 athlon i386 GNU/Linux ####################################### GCA RB40_talairach_2005-07-20.gca AvgCurvTif average.curvature.filled.buckner40.tif GCS curvature.buckner40.filled.desikan_killiany.gcs ####################################### /autofs/space/lucy_002/users/margo/subjects/avm004 Using mgz format

---

Intensity Normalization2 Tue Jan 3 10:09:16 EST 2006 /autofs/space/lucy_002/users/margo/subjects/avm004/mri mri_normalize -mask brain.mgz norm.mgz T1.mgz reading from norm.mgz... zcat: /autofs/space/lucy_002/users/margo/subjects/avm004/mri/norm.mgz.gz: No such file or directory mghRead(/autofs/space/lucy_002/users/margo/subjects/avm004/mri/norm.mgz, -1): read error mri_normalize: could not open source file norm.mgz using MR volume brain.mgz to mask input volume... ERROR: mri_normalize exited with non-zero status Linux tkmeg 2.6.9-22.0.1.ELsmp #1 SMP Thu Oct 27 13:14:25 CDT 2005 i686 athlon i386 GNU/Linux recon-all exited with errors at Tue Jan 3 10:09:17 EST 2006

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer